Add bluster functions to cheatsheet #814
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Given https://github.com/AlexsLemonade/exercise-notebook-answers/pull/228/files#r1861067009, I'm thinking I should go ahead and add |
I was just about to say this. And you may as well add it to the scRNA-seq cheatsheet while you are doing this. |
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@jashapiro done! |
jashapiro
reviewed
Dec 2, 2024
| | Library/Package | Piece of Code | What it's called | What it does | | ||
| |----------------------|--------------------|---------------------|---------------| | ||
| | `bluster`| [`clusterRows()`](https://rdrr.io/bioc/bluster/man/clusterRows.html)| Cluster rows of a matrix | Perform clustering using a variety of algorithms on a matrix-like object | | ||
| | `bluster`| [`KGraphParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering | Run k-means clustering using `kmeans()` when provided to `bluster::clusterRows()` | |
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Clustering function name fix, as well as a clarification that this function only sets up parameters.
Suggested change
| | `bluster`| [`KGraphParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering | Run k-means clustering using `kmeans()` when provided to `bluster::clusterRows()` | | |
| | `bluster`| [`KmeansParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering parameters | Set up parameters to run clustering using `kmeans()` within `bluster::clusterRows()` | |
| |----------------------|--------------------|---------------------|---------------| | ||
| | `bluster`| [`clusterRows()`](https://rdrr.io/bioc/bluster/man/clusterRows.html)| Cluster rows of a matrix | Perform clustering using a variety of algorithms on a matrix-like object | | ||
| | `bluster`| [`KGraphParam()`](https://rdrr.io/bioc/bluster/man/KmeansParam-class.html)| K-means clustering | Run k-means clustering using `kmeans()` when provided to `bluster::clusterRows()` | | ||
| | `bluster`| [`NNGraphParam()`](https://rdrr.io/bioc/bluster/man/NNGraphParam-class.html)| Graph-based clustering | Run community detection algorithms on a nearest-neighbor (NN) graph when provided to `bluster::clusterRows()` | |
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possible rephrasing
Suggested change
| | `bluster`| [`NNGraphParam()`](https://rdrr.io/bioc/bluster/man/NNGraphParam-class.html)| Graph-based clustering | Run community detection algorithms on a nearest-neighbor (NN) graph when provided to `bluster::clusterRows()` | | |
| | `bluster`| [`NNGraphParam()`](https://rdrr.io/bioc/bluster/man/NNGraphParam-class.html)| Graph-based clustering parameters | Set up parameters for nearest-neighbor (NN) graph-based clustering algorithms to be applied within `bluster::clusterRows()` | |
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Closes #813
This PR adds bluster functions used in the (forthcoming) exercise notebook to the
scRNA-seq-advanced.A couple additional questions:
blusterin thescRNA-seqcheatsheet. Should I go ahead and addclusterRows()there too?NNGraphParam()(and/orKGraphParam()KMeansParam()which is also used in thescRNA-seqmodule), so I'll do this all in one go if we want to add more!